QtCreator never finishes parsing pro or source files

Whenever I open our project files in QtCreator (3.5.x or 4.0.0-beta1) in Windows the parsing never finshes and it gets stuck on "Reading Project...". I can open the project just fine in OSX and Linux, but not in Windows. Many of the source files are missing from the project tree and QtCreator never runs the TODO scanner.

Is there any way I can enable some debugging to see what's causing QtCreator to get stuck?